data_6AGP # _model_server_result.job_id 9GLlr5aEHlQ5i6ghzZ2iiQ _model_server_result.datetime_utc '2024-12-22 01:01:10' _model_server_result.server_version 0.9.12 _model_server_result.query_name ligand _model_server_result.source_id pdb-bcif _model_server_result.entry_id 6agp # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":201}' # _entry.id 6AGP # _exptl.entry_id 6AGP _exptl.method 'SOLUTION NMR' # _entity.details ? _entity.formula_weight 443.201 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "GUANOSINE-5'-DIPHOSPHATE" _entity.pdbx_number_of_molecules 1 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation ? _pdbx_struct_oper_list.matrix[1][1] 1 _pdbx_struct_oper_list.matrix[1][2] 0 _pdbx_struct_oper_list.matrix[1][3] 0 _pdbx_struct_oper_list.matrix[2][1] 0 _pdbx_struct_oper_list.matrix[2][2] 1 _pdbx_struct_oper_list.matrix[2][3] 0 _pdbx_struct_oper_list.matrix[3][1] 0 _pdbx_struct_oper_list.matrix[3][2] 0 _pdbx_struct_oper_list.matrix[3][3] 1 _pdbx_struct_oper_list.vector[1] 0 _pdbx_struct_oper_list.vector[2] 0 _pdbx_struct_oper_list.vector[3] 0 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # loop_ _struct_conn.conn_type_id _struct_conn.details _struct_conn.id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_PDB_id _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order metalc ? metalc1 A OG1 THR 17 A THR 17 1_555 C MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.081 ? metalc ? metalc2 B O2B GDP . A GDP 201 1_555 C MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.26 ? # _chem_comp.formula 'C10 H15 N5 O11 P2' _chem_comp.formula_weight 443.201 _chem_comp.id GDP _chem_comp.mon_nstd_flag n _chem_comp.name "GUANOSINE-5'-DIPHOSPHATE" _chem_comp.type 'rna linking' _chem_comp.pdbx_synonyms ? # loop_ _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.comp_id _chem_comp_bond.value_order _chem_comp_bond.pdbx_ordinal _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_aromatic_flag PB O1B GDP doub 83 n n PB O2B GDP sing 84 n n PB O3B GDP sing 85 n n PB O3A GDP sing 86 n n O2B HOB2 GDP sing 87 n n O3B HOB3 GDP sing 88 n n O3A PA GDP sing 89 n n PA O1A GDP doub 90 n n PA O2A GDP sing 91 n n PA O5' GDP sing 92 n n O2A HOA2 GDP sing 93 n n O5' C5' GDP sing 94 n n C5' C4' GDP sing 95 n n C5' H5' GDP sing 96 n n C5' "H5''" GDP sing 97 n n C4' O4' GDP sing 98 n n C4' C3' GDP sing 99 n n C4' H4' GDP sing 100 n n O4' C1' GDP sing 101 n n C3' O3' GDP sing 102 n n C3' C2' GDP sing 103 n n C3' H3' GDP sing 104 n n O3' HO3' GDP sing 105 n n C2' O2' GDP sing 106 n n C2' C1' GDP sing 107 n n C2' H2' GDP sing 108 n n O2' HO2' GDP sing 109 n n C1' N9 GDP sing 110 n n C1' H1' GDP sing 111 n n N9 C8 GDP sing 112 n y N9 C4 GDP sing 113 n y C8 N7 GDP doub 114 n y C8 H8 GDP sing 115 n n N7 C5 GDP sing 116 n y C5 C6 GDP sing 117 n n C5 C4 GDP doub 118 n y C6 O6 GDP doub 119 n n C6 N1 GDP sing 120 n n N1 C2 GDP sing 121 n n N1 HN1 GDP sing 122 n n C2 N2 GDP sing 123 n n C2 N3 GDP doub 124 n n N2 HN21 GDP sing 125 n n N2 HN22 GDP sing 126 n n N3 C4 GDP sing 127 n n # _atom_sites.entry_id 6AGP _atom_sites.fract_transf_matrix[1][1] 1 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 1 _atom_sites.fract_transf_matrix[2][3] 0 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 1 _atom_sites.fract_transf_vector[1] 0 _atom_sites.fract_transf_vector[2] 0 _atom_sites.fract_transf_vector[3] 0 # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_ins_code B 2 GDP A 1 201 182 GDP GDP . C 3 MG A 1 202 183 MG MG . # loop_ _atom_site.group_PDB _atom_site.id _atom_site.type_symbol _atom_site.label_atom_id _atom_site.label_comp_id _atom_site.label_seq_id _atom_site.label_alt_id _atom_site.pdbx_PDB_ins_code _atom_site.label_asym_id _atom_site.label_entity_id _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.occupancy _atom_site.B_iso_or_equiv _atom_site.pdbx_formal_charge _atom_site.auth_atom_id _atom_site.auth_comp_id _atom_site.auth_seq_id _atom_site.auth_asym_id _atom_site.pdbx_PDB_model_num HETATM 1 P PB GDP . . . B 2 34.035 5.899 19.388 1 0 ? PB GDP 201 A 1 HETATM 2 O O1B GDP . . . B 2 33.135 5.729 18.218 1 0 ? O1B GDP 201 A 1 HETATM 3 O O2B GDP . . . B 2 33.49 5.659 20.646 1 0 ? O2B GDP 201 A 1 HETATM 4 O O3B GDP . . . B 2 35.423 5.067 19.149 1 0 ? O3B GDP 201 A 1 HETATM 5 O O3A GDP . . . B 2 34.493 7.405 19.437 1 0 ? O3A GDP 201 A 1 HETATM 6 P PA GDP . . . B 2 34.468 8.508 20.687 1 0 ? PA GDP 201 A 1 HETATM 7 O O1A GDP . . . B 2 33.072 8.734 21.173 1 0 ? O1A GDP 201 A 1 HETATM 8 O O2A GDP . . . B 2 35.423 7.949 21.698 1 0 ? O2A GDP 201 A 1 HETATM 9 O O5' GDP . . . B 2 35.006 9.787 19.974 1 0 ? O5' GDP 201 A 1 HETATM 10 C C5' GDP . . . B 2 36.034 9.775 18.926 1 0 ? C5' GDP 201 A 1 HETATM 11 C C4' GDP . . . B 2 36.63 11.094 18.67 1 0 ? C4' GDP 201 A 1 HETATM 12 O O4' GDP . . . B 2 35.59 11.974 18.016 1 0 ? O4' GDP 201 A 1 HETATM 13 C C3' GDP . . . B 2 36.955 11.923 19.97 1 0 ? C3' GDP 201 A 1 HETATM 14 O O3' GDP . . . B 2 38.164 12.698 19.648 1 0 ? O3' GDP 201 A 1 HETATM 15 C C2' GDP . . . B 2 35.762 12.897 20.226 1 0 ? C2' GDP 201 A 1 HETATM 16 O O2' GDP . . . B 2 35.977 14.12 20.953 1 0 ? O2' GDP 201 A 1 HETATM 17 C C1' GDP . . . B 2 35.258 13.213 18.801 1 0 ? C1' GDP 201 A 1 HETATM 18 N N9 GDP . . . B 2 33.798 13.422 18.705 1 0 ? N9 GDP 201 A 1 HETATM 19 C C8 GDP . . . B 2 32.895 12.352 19.229 1 0 ? C8 GDP 201 A 1 HETATM 20 N N7 GDP . . . B 2 31.728 13.065 18.88 1 0 ? N7 GDP 201 A 1 HETATM 21 C C5 GDP . . . B 2 31.798 14.262 18.299 1 0 ? C5 GDP 201 A 1 HETATM 22 C C6 GDP . . . B 2 31.066 15.334 17.771 1 0 ? C6 GDP 201 A 1 HETATM 23 O O6 GDP . . . B 2 29.732 15.218 17.82 1 0 ? O6 GDP 201 A 1 HETATM 24 N N1 GDP . . . B 2 31.607 16.435 17.236 1 0 ? N1 GDP 201 A 1 HETATM 25 C C2 GDP . . . B 2 33.085 16.531 17.197 1 0 ? C2 GDP 201 A 1 HETATM 26 N N2 GDP . . . B 2 33.409 17.682 16.636 1 0 ? N2 GDP 201 A 1 HETATM 27 N N3 GDP . . . B 2 33.79 15.598 17.652 1 0 ? N3 GDP 201 A 1 HETATM 28 C C4 GDP . . . B 2 33.208 14.521 18.176 1 0 ? C4 GDP 201 A 1 HETATM 29 H HOB3 GDP . . . B 2 36.131 5.568 19.561 1 0 ? HOB3 GDP 201 A 1 HETATM 30 H H5' GDP . . . B 2 35.591 9.4 18 1 0 ? H5' GDP 201 A 1 HETATM 31 H "H5''" GDP . . . B 2 36.832 9.097 19.217 1 0 ? "H5''" GDP 201 A 1 HETATM 32 H H4' GDP . . . B 2 37.547 10.973 18.097 1 0 ? H4' GDP 201 A 1 HETATM 33 H H3' GDP . . . B 2 37.21 11.299 20.822 1 0 ? H3' GDP 201 A 1 HETATM 34 H HO3' GDP . . . B 2 38.739 12.662 20.416 1 0 ? HO3' GDP 201 A 1 HETATM 35 H H2' GDP . . . B 2 34.986 12.307 20.731 1 0 ? H2' GDP 201 A 1 HETATM 36 H HO2' GDP . . . B 2 36.73 13.981 21.528 1 0 ? HO2' GDP 201 A 1 HETATM 37 H H1' GDP . . . B 2 35.78 14.053 18.337 1 0 ? H1' GDP 201 A 1 HETATM 38 H H8 GDP . . . B 2 33.07 11.395 19.698 1 0 ? H8 GDP 201 A 1 HETATM 39 H HN1 GDP . . . B 2 31.027 17.176 16.871 1 0 ? HN1 GDP 201 A 1 HETATM 40 H HN21 GDP . . . B 2 32.685 18.315 16.327 1 0 ? HN21 GDP 201 A 1 HETATM 41 H HN22 GDP . . . B 2 34.381 17.929 16.516 1 0 ? HN22 GDP 201 A 1 # _model_server_stats.io_time_ms 21 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 83 _model_server_stats.query_time_ms 6017 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 41 #